Publications by authors named "Sarah Piché-Choquette"

10 Publications

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Acclimatization of microbial community of submerged membrane bioreactor treating hospital wastewater.

Bioresour Technol 2021 Jan 8;319:124223. Epub 2020 Oct 8.

Investissement Québec - CRIQ, 333, rue Franquet, Quebec, QC G1P 4C7, Canada.

This study was performed to understand the dynamics of the microbial community of submerged membrane bioreactor during the acclimatization process to treat the hospital wastewater. In this regard, three acclimatization phases were examined using a mixture of synthetic wastewater (SWW) and real hospital wastewater (HWW) in the following proportions; In Phase 1: 75:25 v/v (SWW: HWW); Phase 2: 50:50 v/v (SWW: HWW); and Phase 3: 25:75 v/v (SWW: HWW) of wastewater. The microbial community was analyzed using Illumina high throughput sequencing to identify the bacterial and micro-eukaryotes community in SMBR. The acclimatization study clearly demonstrated that shift in microbial community composition with time. The dominance of pathogenic and degrading bacterial communities such as Mycobacterium, Pseudomonas, and Zoogloea was observed at the phase 3 of acclimatization. This study witnessed the major shift in the micro-eukaryotes community, and the proliferation of fungi Basidiomycota was observed in phase 3 of acclimatization.
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http://dx.doi.org/10.1016/j.biortech.2020.124223DOI Listing
January 2021

Microplastic Pollution in China, an Invisible Threat Exacerbated by Food Delivery Services.

Bull Environ Contam Toxicol 2020 Oct 19. Epub 2020 Oct 19.

College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China.

With the rapid development and democratization of the internet and smart phone industry, online food delivery services have become increasingly popular all over the globe, namely in China. One of the unfortunate drawbacks of these delivery services is that they mainly use single-use plastics as food packaging, therefore generating large amounts of disposable food containers to meet demand. Such plastic containers reach the end of their service life after a single meal, and are then discarded as plastic waste. The sheer amount of plastic food containers discarded in this manner exacerbates various environmental issues, including one that is invisible to the naked eye: microplastic pollution. This minireview summarizes the history of food delivery services in China, from orders made face-to-face to digital orders, as well as the consequences introduced by the tremendous amounts of plastic waste generated by the food delivery services. Microplastic pollution could be mitigated to a certain extent by improving the classification, handling and management of single-use plastic containers in China. Furthermore, additional studies focusing on microplastic pollution caused by food delivery services are needed, especially as the use of these services is on the rise worldwide.
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http://dx.doi.org/10.1007/s00128-020-03018-1DOI Listing
October 2020

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies.

Sci Data 2020 07 13;7(1):228. Epub 2020 Jul 13.

Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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http://dx.doi.org/10.1038/s41597-020-0567-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359306PMC
July 2020

Biological H and CO oxidation activities are sensitive to compositional change of soil microbial communities.

Can J Microbiol 2020 Apr 30;66(4):263-273. Epub 2020 Jan 30.

Institut national de la recherche scientifique, Centre Armand Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada.

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO) production, and molecular hydrogen (H) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO production. Soil microcosms with dilution treatments had 58%-98% less H oxidation and 54%-99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H and CO oxidation activities respond to compositional changes of microbial community in soil.
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http://dx.doi.org/10.1139/cjm-2019-0412DOI Listing
April 2020

The bacterial community structure of submerged membrane bioreactor treating synthetic hospital wastewater.

Bioresour Technol 2019 Aug 18;286:121362. Epub 2019 Apr 18.

Centre de Recherche Industrielle du Québec (CRIQ), Quebec, QC, Canada.

The pharmaceuticals are biologically active compounds used to prevent and treat diseases. These pharmaceutical compounds were not fully metabolized by the human body and thus excreted out in the wastewater stream. Thus, the study on the treatment of synthetic hospital wastewater containing pharmaceuticals (ibuprofen, carbamazepine, estradiol and venlafaxine) was conducted to understand the variation of the bacterial community in a submerged membrane bioreactor (SMBR) at varying hydraulic retention time (HRT) of 6, 12 and 18 h. The variation in bacterial community dynamics of SMBR was studied using high throughput sequencing. The removal of pharmaceuticals was uniform at varying HRT. The removal of both ibuprofen and estradiol was accounted for 90%, whereas a lower removal of venlafaxine (<10%) and carbamazepine (>5%) in SMBR was observed. The addition of pharmaceuticals alters the bacterial community structure and result in increased abundance of bacteria (e.g., Flavobacterium, Pedobacter, and Methylibium) reported to degrade toxic pollutant.
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http://dx.doi.org/10.1016/j.biortech.2019.121362DOI Listing
August 2019

Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes.

Appl Environ Microbiol 2019 03 6;85(6). Epub 2019 Mar 6.

INRS-Institut Armand-Frappier, Laval, Québec, Canada.

The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H). H has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H-oxidizing microbes are keystone species driving C cycling along O concentration gradients found in H-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H on C cycling and the C-cycling potential of H-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H as a driver of biogeochemical processes.
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http://dx.doi.org/10.1128/AEM.02418-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6414374PMC
March 2019

Survey of High-Affinity H-Oxidizing Bacteria in Soil Reveals Their Vast Diversity Yet Underrepresentation in Genomic Databases.

Microb Ecol 2017 11 17;74(4):771-775. Epub 2017 Jun 17.

INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada.

While high-affinity H-oxidizing bacteria (HA-HOB) serve as the main sink of atmospheric H, the ecology of this specialist functional group is rather unknown due to its recent discovery. The main purpose of our study is to provide the first extensive survey of HA-HOB in farmland, larch, and poplar soils exposed to 0.5 and 10,000 ppmv H. Using qPCR and qRT-PCR assays along with PCR amplicon high-throughput sequencing of hhyL gene encoding for the large subunit of high-affinity [NiFe]-hydrogenases (HAH), we found that hhyL gene expression ratio explained better variation in measured H oxidation rates than HA-HOB species richness. Carbon, nitrogen, pH, and bacterial species richness appeared as the most important drivers of HA-HOB community structure. Our study also highlights the need to cultivate HA-HOB due to the huge gap in current genomic databases.
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http://dx.doi.org/10.1007/s00248-017-1011-1DOI Listing
November 2017

The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil.

Appl Environ Microbiol 2017 06 17;83(11). Epub 2017 May 17.

INRS-Institut Armand-Frappier, Laval, Québec, Canada

The enrichment of H-oxidizing bacteria (HOB) by H generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. Here we report that the energy potential of H, when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H while enhancing community level carbon substrate utilization potential and lowering CH uptake activity in soil. We found that H triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. We argue that further examination of direct and indirect effects of H on soil microbial communities will lead to a better understanding of the H fertilization effect and soil biogeochemical processes. An innovative dynamic microcosm chamber system was used to demonstrate that H diffusing in soil triggers changes in the distribution of HOB and non-HOB. Although the response was uneven at the taxonomic level, an unexpected coordinated response of microbial functions was observed, including abatement of CH oxidation activity and stimulation of carbon turnover. Our work suggests that elevated H rewires soil biogeochemical structure through a combination of direct effects on the growth and persistence of HOB and indirect effects on a variety of microbial processes involving HOB and non-HOB.
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http://dx.doi.org/10.1128/AEM.00275-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5440700PMC
June 2017

H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups.

PeerJ 2016 10;4:e1782. Epub 2016 Mar 10.

INRS-Institut Armand-Frappier , Laval, Quebec , Canada.

Soil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities.
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http://dx.doi.org/10.7717/peerj.1782DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793312PMC
March 2016